From f0d735cefbbb42c9b1fda6e0df5f80b64a27b1c9 Mon Sep 17 00:00:00 2001
From: Devon Ryan <dpryan79@gmail.com>
Date: Fri, 22 May 2020 21:53:14 +0200
Subject: [PATCH 1/3] Bump version

---
 MBias.c  | 1 +
 Makefile | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/MBias.c b/MBias.c
index 05f08b6..e6f8cad 100644
--- a/MBias.c
+++ b/MBias.c
@@ -301,6 +301,7 @@ int mbias_main(int argc, char *argv[]) {
     config.keepCpG = 1; config.keepCHG = 0; config.keepCHH = 0;
     config.minMapq = 10; config.minPhred = 5; config.keepDupes = 0;
     config.keepSingleton = 0, config.keepDiscordant = 0;
+    config.filterMappability = 0;
     
     config.fp = NULL;
     config.bai = NULL;
diff --git a/Makefile b/Makefile
index 1fc8815..8d884a8 100644
--- a/Makefile
+++ b/Makefile
@@ -11,7 +11,7 @@ CFLAGS ?= -Wall -g -O3 -pthread
 all: MethylDackel
 
 OBJS = common.o bed.o svg.o pileup.o extract.o MBias.o mergeContext.o perRead.o
-VERSION = 0.5.0
+VERSION = 0.5.1
 
 version.h:
 	echo '#define VERSION "$(VERSION)"' > $@

From ba5eb8e9317498aa8de929224e175e4c260bbebc Mon Sep 17 00:00:00 2001
From: Devon Ryan <dpryan79@gmail.com>
Date: Fri, 22 May 2020 21:54:27 +0200
Subject: [PATCH 2/3] Fix #93 and bump to 0.5.1

---
 CHANGELOG.md | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 1a95f1e..d2cb819 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,7 @@
+Version 0.5.1:
+
+   * Fixed an issue in `MethylDackel mbias` due to an uninitialized value (issue #93).
+
 Version 0.5.0:
 
    * Fixed an issue with the `--cytosine_report` option where the reported chromosome name could be wrong IF the input BAM files were very sparse and multiple threads were used. (issue #88)

From dfa5206333594df00f6c6d87e68510b090166b9a Mon Sep 17 00:00:00 2001
From: Devon Ryan <dpryan79@gmail.com>
Date: Sat, 23 May 2020 09:42:02 +0200
Subject: [PATCH 3/3] Prevent out of bounds memory usage

---
 MBias.c  | 2 +-
 common.c | 3 +++
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/MBias.c b/MBias.c
index e6f8cad..c062e8d 100644
--- a/MBias.c
+++ b/MBias.c
@@ -58,7 +58,7 @@ void *extractMBias(void *foo) {
     Config *config = (Config*) foo;
     bam_hdr_t *hdr;
     bam_mplp_t iter;
-    int ret, tid, pos, i, seqlen, rv, o = 0;
+    int ret, tid, pos = 0, i, seqlen, rv, o = 0;
     int32_t bedIdx = 0;
     int strand;
     int n_plp; //This will need to be modified for multiple input files
diff --git a/common.c b/common.c
index 6ab7c9c..740ce95 100644
--- a/common.c
+++ b/common.c
@@ -47,6 +47,7 @@ void print_version() {
 }
 
 inline int isCpG(char *seq, int pos, int seqlen) {
+    if(pos >= seqlen) return 0;
     if(*(seq+pos) == 'C' || *(seq+pos) == 'c') {
         if(pos+1 == seqlen) return 0;
         if(*(seq+pos+1) == 'G' || *(seq+pos+1) == 'g') return 1;
@@ -60,6 +61,7 @@ inline int isCpG(char *seq, int pos, int seqlen) {
 }
 
 inline int isCHG(char *seq, int pos, int seqlen) {
+    if(pos >= seqlen) return 0;
     if(*(seq+pos) == 'C' || *(seq+pos) == 'c') {
         if(pos+2 >= seqlen) return 0;
         if(*(seq+pos+2) == 'G' || *(seq+pos+2) == 'g') return 1;
@@ -73,6 +75,7 @@ inline int isCHG(char *seq, int pos, int seqlen) {
 }
 
 inline int isCHH(char *seq, int pos, int seqlen) {
+    if(pos >= seqlen) return 0;
     if(*(seq+pos) == 'C' || *(seq+pos) == 'c') return 1;
     else if(*(seq+pos) == 'G' || *(seq+pos) == 'g') return -1;
     return 0;